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Figure S1 Rooting the cyanobacterial tree.

Figure S2 Bayesian analyses using a covarion model.

Figure S3 Bootstrap support for SSU–LSU and SSU–RpoC trees.

Figure S4 ASR–RMC chronogram using the 139-gene MB tree.

Figure S5 ASR–RMC chronogram using SSU–RpoC tree with alternative topology A.

Figure S6 ASR–RMC chronogram using SSU–RpoC tree with alternative topology B.

Table S1 Sequence composition of genomic data sets.

Table S2 Accession Numbers for SSU, LSU and RpoC1 data and sequence composition of SSU–LSU and SSU–RpoC data sets.

Table S3 Inferred ancestral cell diameters (in μm) using multiple trees and methods.

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